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- PDB-219d: DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(D... -

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Basic information

Entry
Database: PDB / ID: 219d
TitleDNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT) (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE MOIETY
Components
  • DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3')
  • RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')
KeywordsDNA-RNA HYBRID / DNA / RNA / HYBRID / PHOSPHOROTHIOATE / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsGonzalez, C. / James, T.L.
Citation
Journal: Biochemistry / Year: 1995
Title: Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints.
Authors: Gonzalez, C. / Stec, W. / Reynolds, M.A. / James, T.L.
#1: Journal: Biochemistry / Year: 1994
Title: Structural Study of a DNA(Dot)RNA Hybrid Duplex with a Chiral Phosphorothioate Moiety by NMR: Extraction of Distance and Torsion Angle Constraints and Imino Proton Exchange Rates
Authors: Gonzalez, C. / Stec, W. / Kobylanska, A. / Hogrefe, R.I. / Reynolds, M.A. / James, T.L.
History
DepositionJul 25, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3')
B: RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2222
Polymers6,2222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3')


Mass: 3100.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: RNA chain RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3')


Mass: 3121.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: RIBONUCLEIC ACID

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY MINOR ...Text: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REPRESENT THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE SIXTH ROOT R-FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL NOE DATA, CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND JAMES), HAS A VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION BETWEEN EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING CONSTRAINTS IS 2.01 HZ. THIS POOR FIT OF THE COUPLING CONSTANTS IS DUE TO CONFORMATIONAL FLEXIBILITY IN THE SUGAR RING.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

SoftwareName: AMBER / Classification: refinement
NMR softwareName: AMBER4 / Developer: PEARLMAN,KOLLMAN / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0
NMR ensembleConformers submitted total number: 1

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